Pedroia, 35, has played only six games this season, all in April, and was limited to three games last year.
The Red Sox say Pedroia had knee joint preservation surgery on Tuesday in Colorado. He will begin his rehabilitation in Arizona.
Although Red Sox manager Alex Cora hinted at Pedroia's desire to play again, he told reporters that the second baseman won't be ready to return in 2019.
"As everybody knows, he had a procedure, something to ease the pain or [take the] pain away," Cora said. "Just another step to see if he can feel better and see where it takes us."
Cora added that Pedroia is "going to keep trying to find ways to make this happen, and we'll see where it goes."
Tuesday's procedure was the latest of several surgeries Pedroia has had on the knee since he injured it taking a hard slide from Manny Machado in 2017.
A four-time All-Star and the 2008 AL MVP, Pedroia said in May that he would take an indefinite leave of absence in his struggle to recover from the knee issues, putting in doubt his path back to the big leagues.
The Associated Press contributed to this report.